John Plummer (Jason Lee) is engaged to Elaine (Leslie Mann), and intends to use his life savings of $30,000 to put a down payment on a house. He works for Elain's father, Mr. Warner (Dennis Farina), who already considers John unworthy of his daughter. Simultaneously, John's niece Noreen (Tammy Blanchard), daughter of John's sister, Patty (Megan Mullally), is accepted to Harvard University, but needs an additional $30,000 on top of her grants and scholarships. Noreen shows John an old videotape where he promised to pay for Noreen's college. John now has a moral and financial dilemma – disappoint his fiancée or disappoint his niece and take away her only chance to escape from poverty.

John confides in his friend Walter "Duff" Duffy (Tom Green). Duff, a landscaper, convinces John to steal from one of his rich landscaping clients, who keeps large amounts of cash in an unlocked safe. The pair set off to steal the cash, but Duff runs away when lights come on in the home, leaving John to get caught by Emmett Cook (Richard Jenkins). Cook forces John to cross-dress and role-play the part of Cook's late wife as the two men lie in bed and "spoon". Eventually, after taking an incriminating photograph of John, Cook releases him. As he is leaving, Mr. Warner rides by and takes note of John's panicked behavior, believing that he has caught John in an affair.

Further capers ensue as John and Duff try to rob a liquor store and later attempt to con a drug lord out of $30,000 by concocting a phony story about running an ecstasy ring. A police detective (John C. McGinley) is on to John and Duff, but never has enough evidence to actually pin any of the crimes on them. Meanwhile, Mr. Warner breaks into Cook's residence in order to get evidence against John, and once Cook catches him, he is forced to "spoon" as well. Before leaving, Warner finds the photo of John from the album, which he then gives to Elaine.

John is forced to confess everything to Elaine. Not only is she not upset with John, but she now respects and admires him far more for the lengths he was willing to go to in order to provide for her, spare her feelings and send his niece to Harvard. Elaine then confides in John that her wealthy father keeps a great deal of money at his business, and that it would be easy for them to steal it. John, Elaine, and Duff set out to rob the business in the night. Unfortunately, Mr. Warner had hid his dog Rex inside the vault. Rex latches on to Duff and does not let go. Just as John and Elaine find the money, Mr. Warner tries to attack them but he is caught by the detective who mistakes him for a burglar. John and Elaine escape to Duff's van. The police arrive and the gang unsuccessfully tries to get away. They are all taken into custody by the detective and facing a series of charges including breaking and entering and animal cruelty. John feels like his goose is cooked, until the judge in charge of his arraignment turns out to be the gun-toting Emmett Cook.

Upon their mutual recognition, John writes, in his lawyer's notebook, a message to Cook and flashes it across the court, threatening to expose the judge's fetish; upon reading the makeshift sign, Cook quickly dismisses all charges against John. Finally, Duff comes through as best he can and gives John his life savings, $1,000, which John bets on a longshot horse which wins and which paid 30 to 1. John and Elaine are married, Noreen goes off to college, and, in the final scene, John is left to ponder how loser Duff could possibly accumulate $1,000 – the last scene shows Duff offering to "spoon" with Cook for $1,000.

Stealing Harvard received negative reviews from critics. It currently holds a 9% rating on Rotten Tomatoes based on 103 reviews with the consensus: "There are some laughs in Stealing Harvard, but they are few and far between, and Tom Green's antics grow old fast."